Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin‐Fixed Paraffin‐Embedded Tissue
ABSTRACT Purpose Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end‐stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post‐translational modif...
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| Veröffentlicht in: | Proteomics. Clinical applications 2024-11, Vol.18 (6), p.e202400018-n/a |
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| creator | Schwab, Stefanie K. Harris, Peter S. Michel, Cole McGinnis, Courtney D. Nahomi, Rooban B. Assiri, Mohammed A. Reisdorph, Richard Henriksen, Kammi Orlicky, David J. Levi, Moshe Rosenberg, Avi Nagaraj, Ram H. Fritz, Kristofer S. |
| description | ABSTRACT
Purpose
Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end‐stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post‐translational modifications. Lysine acetylation is associated with cellular metabolic flux and is thought to be altered in patients with diabetes and dysfunctional renal metabolism.
Experimental Design
A novel extraction and LC‐MS/MS approach was adapted to quantify sites of lysine acetylation from formalin‐fixed paraffin‐embedded (FFPE) kidney tissue and from patients with DKD and non‐diabetic donors (n = 5 and n = 7, respectively).
Results
Analysis of FFPE tissues identified 840 total proteins, with 225 of those significantly changing in patients with DKD. Acetylomic analysis quantified 289 acetylated peptides, with 69 of those significantly changing. Pathways impacted in DKD patients revealed numerous metabolic pathways, specifically mitochondrial function, oxidative phosphorylation, and sirtuin signaling. Differential protein acetylation in DKD patients impacted sirtuin signaling, valine, leucine, and isoleucine degradation, lactate metabolism, oxidative phosphorylation, and ketogenesis.
Conclusions and Clinical Relevance
A quantitative acetylomics platform was developed for protein biomarker discovery in formalin‐fixed and paraffin‐embedded biopsies of kidney transplant patients suffering from DKD. |
| doi_str_mv | 10.1002/prca.202400018 |
| format | Article |
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Purpose
Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end‐stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post‐translational modifications. Lysine acetylation is associated with cellular metabolic flux and is thought to be altered in patients with diabetes and dysfunctional renal metabolism.
Experimental Design
A novel extraction and LC‐MS/MS approach was adapted to quantify sites of lysine acetylation from formalin‐fixed paraffin‐embedded (FFPE) kidney tissue and from patients with DKD and non‐diabetic donors (n = 5 and n = 7, respectively).
Results
Analysis of FFPE tissues identified 840 total proteins, with 225 of those significantly changing in patients with DKD. Acetylomic analysis quantified 289 acetylated peptides, with 69 of those significantly changing. Pathways impacted in DKD patients revealed numerous metabolic pathways, specifically mitochondrial function, oxidative phosphorylation, and sirtuin signaling. Differential protein acetylation in DKD patients impacted sirtuin signaling, valine, leucine, and isoleucine degradation, lactate metabolism, oxidative phosphorylation, and ketogenesis.
Conclusions and Clinical Relevance
A quantitative acetylomics platform was developed for protein biomarker discovery in formalin‐fixed and paraffin‐embedded biopsies of kidney transplant patients suffering from DKD.</description><identifier>ISSN: 1862-8346</identifier><identifier>ISSN: 1862-8354</identifier><identifier>EISSN: 1862-8354</identifier><identifier>DOI: 10.1002/prca.202400018</identifier><identifier>PMID: 38923810</identifier><language>eng</language><publisher>Germany: Wiley Subscription Services, Inc</publisher><subject>Acetylation ; Biomarkers ; Biopsy ; Chromatography, Liquid ; Design of experiments ; Diabetes ; Diabetes mellitus ; Diabetic Nephropathies - metabolism ; Diabetic Nephropathies - pathology ; Female ; Formaldehyde ; formalin‐fixed paraffin‐embedded ; Humans ; Isoleucine ; Ketogenesis ; Kidney - metabolism ; Kidney - pathology ; kidney disease ; Kidney diseases ; Kidney transplantation ; Leucine ; Lysine ; Lysine - metabolism ; Male ; Metabolic flux ; Metabolic pathways ; Metabolism ; Middle Aged ; Nephropathy ; Oxidative metabolism ; Oxidative phosphorylation ; Paraffin ; Paraffin Embedding ; Paraffins ; Peptides ; Phosphorylation ; Protein Processing, Post-Translational ; Protein turnover ; Proteins ; Proteomics ; Renal function ; Signal transduction ; Tandem Mass Spectrometry ; Tissue Fixation ; Valine</subject><ispartof>Proteomics. Clinical applications, 2024-11, Vol.18 (6), p.e202400018-n/a</ispartof><rights>2024 Wiley‐VCH GmbH.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c2531-df2f905b55ec46e195cd8a4fe04767e4ed1d4ad5a0f1330df81c05c79bbcb6183</cites><orcidid>0000-0002-1499-6174 ; 0000-0002-0417-1400</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fprca.202400018$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fprca.202400018$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1416,27922,27923,45572,45573</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38923810$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Schwab, Stefanie K.</creatorcontrib><creatorcontrib>Harris, Peter S.</creatorcontrib><creatorcontrib>Michel, Cole</creatorcontrib><creatorcontrib>McGinnis, Courtney D.</creatorcontrib><creatorcontrib>Nahomi, Rooban B.</creatorcontrib><creatorcontrib>Assiri, Mohammed A.</creatorcontrib><creatorcontrib>Reisdorph, Richard</creatorcontrib><creatorcontrib>Henriksen, Kammi</creatorcontrib><creatorcontrib>Orlicky, David J.</creatorcontrib><creatorcontrib>Levi, Moshe</creatorcontrib><creatorcontrib>Rosenberg, Avi</creatorcontrib><creatorcontrib>Nagaraj, Ram H.</creatorcontrib><creatorcontrib>Fritz, Kristofer S.</creatorcontrib><title>Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin‐Fixed Paraffin‐Embedded Tissue</title><title>Proteomics. Clinical applications</title><addtitle>Proteomics Clin Appl</addtitle><description>ABSTRACT
Purpose
Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end‐stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post‐translational modifications. Lysine acetylation is associated with cellular metabolic flux and is thought to be altered in patients with diabetes and dysfunctional renal metabolism.
Experimental Design
A novel extraction and LC‐MS/MS approach was adapted to quantify sites of lysine acetylation from formalin‐fixed paraffin‐embedded (FFPE) kidney tissue and from patients with DKD and non‐diabetic donors (n = 5 and n = 7, respectively).
Results
Analysis of FFPE tissues identified 840 total proteins, with 225 of those significantly changing in patients with DKD. Acetylomic analysis quantified 289 acetylated peptides, with 69 of those significantly changing. Pathways impacted in DKD patients revealed numerous metabolic pathways, specifically mitochondrial function, oxidative phosphorylation, and sirtuin signaling. Differential protein acetylation in DKD patients impacted sirtuin signaling, valine, leucine, and isoleucine degradation, lactate metabolism, oxidative phosphorylation, and ketogenesis.
Conclusions and Clinical Relevance
A quantitative acetylomics platform was developed for protein biomarker discovery in formalin‐fixed and paraffin‐embedded biopsies of kidney transplant patients suffering from DKD.</description><subject>Acetylation</subject><subject>Biomarkers</subject><subject>Biopsy</subject><subject>Chromatography, Liquid</subject><subject>Design of experiments</subject><subject>Diabetes</subject><subject>Diabetes mellitus</subject><subject>Diabetic Nephropathies - metabolism</subject><subject>Diabetic Nephropathies - pathology</subject><subject>Female</subject><subject>Formaldehyde</subject><subject>formalin‐fixed paraffin‐embedded</subject><subject>Humans</subject><subject>Isoleucine</subject><subject>Ketogenesis</subject><subject>Kidney - metabolism</subject><subject>Kidney - pathology</subject><subject>kidney disease</subject><subject>Kidney diseases</subject><subject>Kidney transplantation</subject><subject>Leucine</subject><subject>Lysine</subject><subject>Lysine - metabolism</subject><subject>Male</subject><subject>Metabolic flux</subject><subject>Metabolic pathways</subject><subject>Metabolism</subject><subject>Middle Aged</subject><subject>Nephropathy</subject><subject>Oxidative metabolism</subject><subject>Oxidative phosphorylation</subject><subject>Paraffin</subject><subject>Paraffin Embedding</subject><subject>Paraffins</subject><subject>Peptides</subject><subject>Phosphorylation</subject><subject>Protein Processing, Post-Translational</subject><subject>Protein turnover</subject><subject>Proteins</subject><subject>Proteomics</subject><subject>Renal function</subject><subject>Signal transduction</subject><subject>Tandem Mass Spectrometry</subject><subject>Tissue Fixation</subject><subject>Valine</subject><issn>1862-8346</issn><issn>1862-8354</issn><issn>1862-8354</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc9u1DAQxi0EoqVw5YgiceGyy_hf4hxX2y4gVbCgcrYce8y6SuJgJ4LceASekSchZcseuHCamU-_-TSaj5DnFNYUgL0ekjVrBkwAAFUPyDlVJVspLsXDUy_KM_Ik51sAKVgFj8kZVzXjisI5OXycTD8GP4f-S7FPccTQFxuL49yaMcS-WMbLYBocgy3e43BIcTDjYS58il2xi6kzbeh__fi5C9_RFXuTjPd_hKuuQecW7SbkPOFT8sibNuOz-3pBPu-ubrZvV9cf3rzbbq5XlklOV84zX4NspEQrSqS1tE4Z4RFEVVYo0FEnjJMGPOUcnFfUgrRV3TS2KaniF-TV0XdI8euEedRdyBbb1vQYp6w5VKyqlWJ8QV_-g97GKfXLdZpTphitKygXan2kbIo5J_R6SKEzadYU9F0G-i4DfcpgWXhxbzs1HboT_vfpCyCOwLfQ4vwfO73_tN0wDpT_BmtnlPI</recordid><startdate>202411</startdate><enddate>202411</enddate><creator>Schwab, Stefanie K.</creator><creator>Harris, Peter S.</creator><creator>Michel, Cole</creator><creator>McGinnis, Courtney D.</creator><creator>Nahomi, Rooban B.</creator><creator>Assiri, Mohammed A.</creator><creator>Reisdorph, Richard</creator><creator>Henriksen, Kammi</creator><creator>Orlicky, David J.</creator><creator>Levi, Moshe</creator><creator>Rosenberg, Avi</creator><creator>Nagaraj, Ram H.</creator><creator>Fritz, Kristofer S.</creator><general>Wiley Subscription Services, Inc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>8FD</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-1499-6174</orcidid><orcidid>https://orcid.org/0000-0002-0417-1400</orcidid></search><sort><creationdate>202411</creationdate><title>Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin‐Fixed Paraffin‐Embedded Tissue</title><author>Schwab, Stefanie K. ; Harris, Peter S. ; Michel, Cole ; McGinnis, Courtney D. ; Nahomi, Rooban B. ; Assiri, Mohammed A. ; Reisdorph, Richard ; Henriksen, Kammi ; Orlicky, David J. ; Levi, Moshe ; Rosenberg, Avi ; Nagaraj, Ram H. ; Fritz, Kristofer S.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c2531-df2f905b55ec46e195cd8a4fe04767e4ed1d4ad5a0f1330df81c05c79bbcb6183</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Acetylation</topic><topic>Biomarkers</topic><topic>Biopsy</topic><topic>Chromatography, Liquid</topic><topic>Design of experiments</topic><topic>Diabetes</topic><topic>Diabetes mellitus</topic><topic>Diabetic Nephropathies - metabolism</topic><topic>Diabetic Nephropathies - pathology</topic><topic>Female</topic><topic>Formaldehyde</topic><topic>formalin‐fixed paraffin‐embedded</topic><topic>Humans</topic><topic>Isoleucine</topic><topic>Ketogenesis</topic><topic>Kidney - metabolism</topic><topic>Kidney - pathology</topic><topic>kidney disease</topic><topic>Kidney diseases</topic><topic>Kidney transplantation</topic><topic>Leucine</topic><topic>Lysine</topic><topic>Lysine - metabolism</topic><topic>Male</topic><topic>Metabolic flux</topic><topic>Metabolic pathways</topic><topic>Metabolism</topic><topic>Middle Aged</topic><topic>Nephropathy</topic><topic>Oxidative metabolism</topic><topic>Oxidative phosphorylation</topic><topic>Paraffin</topic><topic>Paraffin Embedding</topic><topic>Paraffins</topic><topic>Peptides</topic><topic>Phosphorylation</topic><topic>Protein Processing, Post-Translational</topic><topic>Protein turnover</topic><topic>Proteins</topic><topic>Proteomics</topic><topic>Renal function</topic><topic>Signal transduction</topic><topic>Tandem Mass Spectrometry</topic><topic>Tissue Fixation</topic><topic>Valine</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Schwab, Stefanie K.</creatorcontrib><creatorcontrib>Harris, Peter S.</creatorcontrib><creatorcontrib>Michel, Cole</creatorcontrib><creatorcontrib>McGinnis, Courtney D.</creatorcontrib><creatorcontrib>Nahomi, Rooban B.</creatorcontrib><creatorcontrib>Assiri, Mohammed A.</creatorcontrib><creatorcontrib>Reisdorph, Richard</creatorcontrib><creatorcontrib>Henriksen, Kammi</creatorcontrib><creatorcontrib>Orlicky, David J.</creatorcontrib><creatorcontrib>Levi, Moshe</creatorcontrib><creatorcontrib>Rosenberg, Avi</creatorcontrib><creatorcontrib>Nagaraj, Ram H.</creatorcontrib><creatorcontrib>Fritz, Kristofer S.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Immunology Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Proteomics. Clinical applications</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Schwab, Stefanie K.</au><au>Harris, Peter S.</au><au>Michel, Cole</au><au>McGinnis, Courtney D.</au><au>Nahomi, Rooban B.</au><au>Assiri, Mohammed A.</au><au>Reisdorph, Richard</au><au>Henriksen, Kammi</au><au>Orlicky, David J.</au><au>Levi, Moshe</au><au>Rosenberg, Avi</au><au>Nagaraj, Ram H.</au><au>Fritz, Kristofer S.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin‐Fixed Paraffin‐Embedded Tissue</atitle><jtitle>Proteomics. Clinical applications</jtitle><addtitle>Proteomics Clin Appl</addtitle><date>2024-11</date><risdate>2024</risdate><volume>18</volume><issue>6</issue><spage>e202400018</spage><epage>n/a</epage><pages>e202400018-n/a</pages><issn>1862-8346</issn><issn>1862-8354</issn><eissn>1862-8354</eissn><abstract>ABSTRACT
Purpose
Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end‐stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post‐translational modifications. Lysine acetylation is associated with cellular metabolic flux and is thought to be altered in patients with diabetes and dysfunctional renal metabolism.
Experimental Design
A novel extraction and LC‐MS/MS approach was adapted to quantify sites of lysine acetylation from formalin‐fixed paraffin‐embedded (FFPE) kidney tissue and from patients with DKD and non‐diabetic donors (n = 5 and n = 7, respectively).
Results
Analysis of FFPE tissues identified 840 total proteins, with 225 of those significantly changing in patients with DKD. Acetylomic analysis quantified 289 acetylated peptides, with 69 of those significantly changing. Pathways impacted in DKD patients revealed numerous metabolic pathways, specifically mitochondrial function, oxidative phosphorylation, and sirtuin signaling. Differential protein acetylation in DKD patients impacted sirtuin signaling, valine, leucine, and isoleucine degradation, lactate metabolism, oxidative phosphorylation, and ketogenesis.
Conclusions and Clinical Relevance
A quantitative acetylomics platform was developed for protein biomarker discovery in formalin‐fixed and paraffin‐embedded biopsies of kidney transplant patients suffering from DKD.</abstract><cop>Germany</cop><pub>Wiley Subscription Services, Inc</pub><pmid>38923810</pmid><doi>10.1002/prca.202400018</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-1499-6174</orcidid><orcidid>https://orcid.org/0000-0002-0417-1400</orcidid></addata></record> |
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| subjects | Acetylation Biomarkers Biopsy Chromatography, Liquid Design of experiments Diabetes Diabetes mellitus Diabetic Nephropathies - metabolism Diabetic Nephropathies - pathology Female Formaldehyde formalin‐fixed paraffin‐embedded Humans Isoleucine Ketogenesis Kidney - metabolism Kidney - pathology kidney disease Kidney diseases Kidney transplantation Leucine Lysine Lysine - metabolism Male Metabolic flux Metabolic pathways Metabolism Middle Aged Nephropathy Oxidative metabolism Oxidative phosphorylation Paraffin Paraffin Embedding Paraffins Peptides Phosphorylation Protein Processing, Post-Translational Protein turnover Proteins Proteomics Renal function Signal transduction Tandem Mass Spectrometry Tissue Fixation Valine |
| title | Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin‐Fixed Paraffin‐Embedded Tissue |
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